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Get oncology-relevant phenotype terms

Source: R/get_terms.R
get_terms.Rd

Downloads and returns a dataset with an expanded set of oncology-relevant phenotype terms (UMLS), using OncoTree as a starting point. The expansion has been conducted by tracking the MeSH/UMLS tree structure with phenotype terms. Each record comes with cross-references to Disease Ontology (DO), Experimental Factor Ontology (EFO), and ICD10 wherever available. The dataset comes as a list object, with two elements:

  • metadata - a data frame with metadata regarding annotation resources used

  • records - a data frame with phenotype terms

Usage

get_terms(
  cache_dir = NA,
  force_download = FALSE,
  site = NA,
  ignore_minor_type = FALSE
)

Arguments

cache_dir

Local directory for data download

force_download

Logical indicating if local cache should be overwritten (set to TRUE to re-download if file exists in cache)

site

limit phenotype terms to those relevant for a given primary tumor type/site. Possible values: 'Adrenal Gland', 'Ampulla of Vater', 'Biliary Tract', 'Bladder/Urinary Tract', 'Bone', 'Breast', 'Cervix', 'CNS/Brain', 'Colon/Rectum', 'Esophagus/Stomach', 'Eye', 'Head and Neck', 'Kidney', 'Liver', 'Lung', 'Lymphoid', 'Myeloid', 'Other/Unknown', 'Ovary/Fallopian Tube', 'Pancreas', 'Penis', 'Peripheral Nervous System', 'Peritoneum', 'Pleura', 'Prostate', 'Skin', 'Soft Tissue', 'Testis', 'Thymus', 'Thyroid', 'Uterus', 'Vulva/Vagina'

ignore_minor_type

logical indicating if minor tumor types should be excluded or not

Value

metadata - A data frame with 5 rows and 6 columns:

  • source - gene annotation source

  • annotation_data - type of annotations used

  • url - URL of annotation resource

  • citation - publication to cite for annotation source (citation; PMID)

  • version - version used

  • abbreviation - abbreviation used in column names of records

records - A data frame the following columns:

  • primary_site - Primary tumor type/site

  • ot_main_type - Main tumor type (OncoTree)

  • ot_name - Phenotype name (OncoTree)

  • ot_level - Tree level (OncoTree)

  • ot_code - Phenotype code (OncoTree)

  • ot_code_path - Tree code path (OncoTree)

  • cui - Concept unique identifier (UMLS)

  • cui_name - Phenotype name (UMLS)

  • efo_id - EFO identifier

  • efo_name - EFO name

  • do_id - DO identifier

  • do_name - DO name

  • do_cancer_slim - DO identifier part of DO cancer slim dictionary (TRUE/FALSE)

  • minor_type - logical indicating whether the term is part of a minor tumor type/site

  • icd10_code - ICD10 identifier

  • source - term indicating the dataset source

Examples


if (FALSE) { # \dontrun{
library(phenOncoX)
oncology_terms <- get_terms(cache_dir = tempdir())
} # }